From 2a7b6eed4a7d64a9ff597a1599544019e8ad2561 Mon Sep 17 00:00:00 2001
From: jws52 <jws52@cam.ac.uk>
Date: Tue, 9 Jul 2024 16:21:45 +0100
Subject: [PATCH] refactor: do not convert units in epi processor
This is handles by ews-epidemiology's model.py
---
ews/coordinator/processor_epidemiology.py | 27 ++++-------------------
1 file changed, 4 insertions(+), 23 deletions(-)
diff --git a/ews/coordinator/processor_epidemiology.py b/ews/coordinator/processor_epidemiology.py
index b9380fd..3be407f 100644
--- a/ews/coordinator/processor_epidemiology.py
+++ b/ews/coordinator/processor_epidemiology.py
@@ -582,35 +582,16 @@ class ProcessorEpidemiology(ProcessorBase):
for epiconf in config_epi['Epi']:
- outfile = epiconf["infectionRasterFileName"]+'_progression.csv'
+ unit_description = ''
+ if epiconf.get('rescale_output_by_host_raster',False) is True:
+ unit_description = '_per_ha_wheat'
+ outfile = f"{epiconf['infectionRasterFileName']}{unit_description}_progression.csv"
# load the full epi results
df_full = read_csv(outfile,header=[0],index_col=[0,1])
column_date_fmt = f"{config_epi['StartTimeShort']}_%Y%m%d%H%M"
df_full_dates = to_datetime(df_full.columns.astype('str'),format=column_date_fmt)
- unit_description = ''
-
- # convert units from ha_infected/ha_cell to ha_infected/ha_wheat
-
- if epiconf['rescale_output_by_host_raster'] is True:
-
- unit_description = '_per_ha_wheat'
-
- model_colns = df_full.columns
-
- df_full = self.get_model_divided_by_host_fraction(
- df_full,
- config_epi['Host']['HostCSV'],
- model_colns = model_colns)
-
- # save to csv
- outfile_hawheat = f"{epiconf['infectionRasterFileName']}{unit_description}_progression.csv"
- df_full.to_csv(outfile_hawheat,header=True,index=True)
-
- outfile_hawheat_final = f"{epiconf['infectionRasterFileName']}{unit_description}.csv"
- df_full.iloc[:,-1].to_csv(outfile_hawheat_final,header=True,index=True)
-
# determine date to cut with
# plus 1 minute so midnight is associated with preceding day
date_to_cut = datetime.datetime.strptime(config_epi['StartString']+'0001','%Y%m%d%H%M')
--
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